Hi, I'm trying to apply some distance restraints to several H-bonds in my systems (all in protein) . Due to manual I added following lines [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 3880 4829 1 0 1 0.0 0.22 0.4 1.0 3880 7692 1 0 1 0.0 0.22 0.4 1.0 4820 6654 1 1 1 0.0 0.22 0.4 1.0 4820 6700 1 1 1 0.0 0.22 0.4 1.0 6652 6889 1 2 1 0.0 0.22 0.4 1.0 6652 6856 1 2 1 0.0 0.22 0.4 1.0 in itp. file
and following lines disre = simple disre_weighting = equal disre_mixed = no disre_fc = 1000 disre_tau = 0 in .mdp file. Next md simulation run fine and after it I see Dist.-Rest. option when executing g_energy, but I don't see any distinct influence on trajectory - all restrainted distances seems to be free and sometimes even exceeding 4 angstrom. I tried to change index, type', disre_fc values from 1000 to 200000, but nothing helped. Besides that when I'm trying to use g_disre I'm getting following error - 'Segmentation fault' So what's wrong and how can I be sure that distance restraints works? thanks in advance.
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